Exploratory differential gene expression analysis in microarray experiments with no or limited replication

Loguinov, Alexander V; Mian, I Saira; Vulpe, Chris D

doi:10.1186/gb-2004-5-3-r18

Table 2 Candidate differential expressed genes with different approaches

From: Exploratory differential gene expression analysis in microarray experiments with no or limited replication

RN	ORF name	STI1	STI2	smuSTI1	smuSTI2	adsmuSTI1	adsmuSTI2
1	YBR047W			+	+	+
2	YBR207W	+	+	+	+	+	+
3	YBR295W			+	+	+	+
4	YDR264C	+		+	+	+	+
5	YDR269C			+	+
6	YDR270W	+	+	+	+	+	+
7	YDR441C			+	+
8	YDR476C	+		+	+	+	+
9	YDR534C	+	+	+	+	+	+
10	YEL065W	+	+	+	+	+	+
11	YER145C	+	+	+	+	+	+
12	YFL041W	+		+	+	+	+
13	YFR023W			+
14	YFR024C-A			+
15	YGL015C	+	+	+	+	+	+
16	YGL039W	+	+	+	+	+	+
17	YGL055W			+
18	YGR065C			+	+	+	+
19	YGR079W			+	+	+
20	YGR257C			+	+
21	YHL035C	+	+	+	+	+	+
22	YHL040C	+	+	+	+	+	+
23	YHL047C	+	+	+	+	+	+
24	YHR042W			+	+	+	+
25	YHR175W	+	+	+	+	+	+
26	YJL145W			+
27	YJL153C			+	+	+	+
28	YKL039W			+
29	YKL220C	+	+	+	+	+	+
30	YKR052C			+	+	+
31	YLL051C	+	+	+	+	+	+
32	YLL053C			+	+	+
33	YLR034C			+	+	+	+
34	YLR046C			+	+	+	+
35	YLR056W			+	+	+	+
36	YLR126C	+	+	+	+	+	+
37	YLR127C			+	+
38	YLR136C	+		+	+	+	+
39	YLR192C			+
40	YLR205C	+	+	+	+	+	+
41	YLR214W	+	+	+	+	+	+
42	YMR006C			+	+	+	+
43	YMR011W			+	+	+	+
44	YMR058W	+	+	+	+	+	+
45	YMR251W	+	+	+	+	+	+
46	YMR319C			+	+
47	YNL237W	+	+	+	+	+	+
48	YNL259C	+	+	+	+	+	+
49	YNR056C	+	+	+	+	+	+
50	YNR060W	+	+	+	+	+	+
51	YOL153C	+	+	+	+	+
52	YOL158C	+	+	+	+	+	+
53	YOR334W			+	+	+	+
54	YOR381W	+	+	+	+	+	+
55	YOR382W	+	+	+	+	+	+
56	YOR383C	+	+	+	+	+	+
57	YOR384W	+	+	+	+	+	+
58	YPL171C			+
59	YBR250W			+
60	YDR423C			+
61	YER028C			+
62	YHR199C			+
63	YIL169C			+
64	YJL149W			+	+	+
65	YOL101C			+		+
66	YOL164W			+		+
RN	ORF name	STI1	STI2	smuSTI1	smuSTI2	adsmuSTI1	adsmuSTI2
1	YBR054W	+		+	+	+	+
2	YBR145W			+
3	YBR147W			+	+	+	+
4	YCL030C	+		+	+	+	+
5	YDL171C	+		+	+	+	+
6	YDR035W			+	+	+
7	YDR234W			+	+
8	YEL039C			+	+	+	+
9	YER001W			+
10	YER156C			+	+
11	YER174C	+		+	+	+	+
12	YFL014W	+		+	+	+	+
13	YFR030W	+	+	+	+	+	+
14	YFR055W			+	+	+	+
15	YGL009C	+	+	+	+	+	+
16	YGL117W	+	+	+	+	+	+
17	YGR088W			+	+	+	+
18	YGR286C	+	+	+	+	+	+
19	YHL021C	+	+	+	+	+	+
20	YHL028W			+	+	+
21	YHR018C	+		+	+	+
22	YHR029C			+
23	YHR045W			+
24	YIL111W			+	+
25	YJL048C			+	+	+
26	YJL088W			+	+
27	YJL089W			+	+
28	YJL200C			+	+	+
29	YJR016C			+
30	YJR025C			+
31	YJR109C			+	+	+
32	YJR137C	+		+	+	+	+
33	YKL062W			+	+	+
34	YKL109W			+	+	+
35	YKL141W			+	+	+
36	YKL148C			+	+	+	+
37	YKL218C			+
38	YKR066C			+	+	+
39	YLL041C	+		+	+	+	+
40	YLR220W			+	+	+
41	YLR304C	+		+	+	+	+
42	YMR021C	+	+	+	+	+	+
43	YMR022W			+	+	+
44	YMR095C			+
45	YMR096W			+	+	+
46	YMR271C			+	+
47	YNL160W			+
48	YOL058W			+	+	+
49	YOL064C			+	+
50	YOR065W			+	+	+
51	YOR195W			+	+
52	YOR230W			+
53	YOR356W			+	+	+	+
54	YPL092W			+	+	+
55	YPR123C			+	+	+
56	YPR160W			+	+
57	YCR106W			+
58	YGR052W			+
59	YJR130C			+
60	YOL119C			+
61	YPL123C			+
62	YPR167C			+
Total		47	34	128	98	84	61

Candidates for differentially-expressed genes in the mac1 cDNA microarray experiment based on three different approaches: STI1 is ordinary STI at 99.98% and STI2, at 99.998%; smuSTI1 is supsmu-based STI at 99.98% and smuSTI2, at 99.998%; adsmuSTI1 is adjusted supsmu-based STI at 99.98% and adsmuSTI2, at 99.998%. The study monitored transcripts in a mac1 knockout and wild type S. cerevisiae. For the STIs, the above-mentioned captured portions of the respective normal distributions were covered with probability at least 99.99%.

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